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public interface State
This interface declares the methods of any state used in a hidden Markov model.
AbstractHMM
Method Summary | |
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String |
getGraphvizNodeOptions(double weight,
double maxWeight,
NumberFormat nf)
This method returns a String representation of the node options that
can be used in Graphviz to create the node for this state. |
double |
getLogScoreFor(int startPos,
int endPos,
Sequence seq)
This method returns the logarithm of the score for a given sequence with given start and end position. |
boolean |
isSilent()
This method returns whether a state is silent or not. |
Method Detail |
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double getLogScoreFor(int startPos, int endPos, Sequence seq) throws WrongLengthException, OperationNotSupportedException
startPos
- the start position within the sequence(s)endPos
- the end position within the sequence(s)seq
- the sequence(s)
WrongLengthException
- if the length can not be modeled
OperationNotSupportedException
- if the reverse complement of the sequence can not be computedString getGraphvizNodeOptions(double weight, double maxWeight, NumberFormat nf)
String
representation of the node options that
can be used in Graphviz to create the node for this state.
weight
- for statemaxWeight
- the maximal weight for the statenf
- the NumberFormat
for the output, can be null
String
representation of the stateboolean isSilent()
true
if the state is silent, otherwise false
SilentEmission
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